In March 1644 Poyer led a force that captured Carew Castle from the Royalists. When, in 1647, he was commanded to disband his army and surrender Pembroke Castle, he refused to do so on the grounds that he was owed money. In April 1648 he was contacted by the Prince of Wales and, with the support of other local Parliamentary commanders, Rowland Laugharne and Rice Powell, he joined a Royalist rebellion, culminating in the Battle of St Fagans.
The remaining forces, besieged by Oliver Cromwell himself at Pembroke, surrendered on 11 July 1648, and Poyer, Laugharne and Powell were condemned to death. It was agreed that only one would face the firing squad, and the three men drew lots, with Poyer being the loser. He was executed at Covent Garden, London. Following the Restoration of the monarchy, his widow was paid a pension of £300 a year by King Charles II of England.